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Expert C4 Context-level documentation specialist. Creates high-level system context diagrams, documents personas, user journeys, system features, and external dependencies.

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Generate comprehensive C4 architecture documentation for an existing repository/codebase using a bottom-up analysis approach.

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Expert C4 Container-level documentation specialist.

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Expert C4 Component-level documentation specialist. Synthesizes C4 Code-level documentation into Component-level architecture, defining component boundaries, interfaces, and relationships.

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Generate comprehensive, developer-friendly API documentation from code, including endpoints, parameters, examples, and best practices

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API documentation workflow for generating OpenAPI specs, creating developer guides, and maintaining comprehensive API documentation.

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This skill should be used when the user asks to "create AGENTS.md", "update AGENTS.md", "maintain agent docs", "set up CLAUDE.md", or needs to keep agent instructions concise. Enforces research-backed best practices for minimal, high-signal agent documentation.

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Predict peptide-MHC class I binding and natural presentation with MHCflurry, NetMHCpan-4.1, and MixMHCpred to nominate candidate CD8 T-cell epitopes. Covers the binding-affinity (BA) vs eluted-ligand (EL/presentation) distinction, why %Rank beats raw nM for cross-allele work, the MS abundance bias that misranks low-expression neoantigens, allele-coverage inequity, and length bias. Use when scanning a protein or peptide set for class I epitopes, scoring neoantigen candidates, or choosing a binding predictor. For CD4/HLA class II see mhc-class-ii-prediction.

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Maps between gene identifier systems (Ensembl, Entrez, HGNC symbol, UniProt, RefSeq, MANE) using AnnotationDbi, biomaRt, mygene, pyensembl, and Ensembl REST. Encodes Ensembl version stripping with GENCODE _PAR_Y preservation, the Ziemann 2016 Excel autocorrect debacle and Bruford 2020 HGNC renames (SEPT*->SEPTIN*, MARCH*->MARCHF*, MARC*->MTARC*, DEC1->DELEC1), OCT4/POU5F1 alias resolution, biomaRt archive endpoints for release pinning, the `filters` (plural) gotcha, MANE Select for clinical reporting, cross-species orthology via Ensembl Compara / OMA / OrthoDB, and tx2gene construction for tximport. Use when converting gene IDs across systems, handling renamed symbols, building tx2gene, pinning to a specific Ensembl release for reproducibility, or mapping cross-species orthologs.

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Quality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and Spearman concordance, essentialome precision-recall AUC against CEGv2 (Hart 2017), Cas9 cut-toxicity diagnostics, copy-number amplicon detection (Aguirre 2016 / Munoz 2016), bottleneck propagation through plasmid pool, infection, selection, and endpoint stages, MOI verification, and DepMap-style screen-quality scoring. Use when assessing screen quality before hit calling, deciding whether to repeat or rescue a screen, diagnosing low-confidence hits, choosing between MAGeCK / BAGEL2 / Chronos based on quality grade, picking a normalization strategy from QC signatures, or evaluating whether an in-vivo screen retained adequate library complexity.

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Use this skill to understand when electronic records are acceptable to FMCSA inspectors. Covers PDF, original-format, and search-ability requirements.

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Use this skill to develop the capability to investigate crashes internally. Covers what to look for, when to escalate to outside experts, and documentation standards.

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Use this skill when a driver encounters adverse weather, road, or traffic conditions and needs to extend driving time. Covers eligibility criteria, the 2-hour maximum extension, documentation requirements, and what does NOT qualify.

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Use this skill to understand FMCSA cardiac certification standards. Covers what cardiac conditions disqualify, time-to-clearance, and what documentation is needed for examiner certification.

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Use this skill when a driver is operating under the 150 air-mile short-haul exception and is asked to produce records. Covers the simplified time records required, when ELD is NOT required, and the documentation that satisfies inspectors.

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Use this skill when a driver wants to use a CMV for personal travel after duty hours. Covers what qualifies as legitimate personal conveyance vs. work-related driving, FMCSA guidance on lodging/meals/home travel, and documentation requirements.

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Use this skill when a driver needs to extend the 14-hour duty window using the 16-hour exception under § 395.1(o). Covers eligibility, frequency limits (once per 7 days), return-to-terminal requirement, and documentation.

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Use this skill when a driver does not meet federal medical standards and needs to apply for a variance. Covers application steps, required documentation, and review timeline.

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Use when a manager, dispatcher, or safety director needs to have a coaching conversation with a driver — about a safety event (harsh brake, hard turn, distraction), an HOS violation, a customer complaint, a missed delivery, repeated minor incidents, or to deliver positive recognition. Covers conversation structure, language, documentation, and escalation.

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Use this skill to document crashes that don't qualify as DOT-recordable. Covers what to track, why it matters, and insurance/CSA implications.

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Organizing digital life for legacy, emergency access, and death preparedness. Specializes in password management, account documentation, digital asset preservation, and ensuring loved ones can access what they need.

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Generate, fill, and assemble PDF documents at scale. Handles legal forms, contracts, invoices, certificates. Supports form filling (pdf-lib), template rendering (Puppeteer, LaTeX), digital signatures (DocuSign), and document assembly. Use for legal tech, HR automation, invoice generation. Activate on "PDF generation", "form filling", "document automation", "digital signatures". NOT for simple PDF viewing, basic file conversion, or OCR text extraction.

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Expert in developer tool documentation as a product. Activate on: docs site, getting started guide, API reference, developer documentation, Docusaurus, Mintlify, Nextra, ReadMe, migration guide, troubleshooting page, docs information architecture, documentation testing, llms.txt. NOT for: marketing copy (use seo-content-blogging), API design itself (use api-architect), general technical writing (use technical-writer).

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Handle mental health crisis situations in AI coaching safely. Use when implementing crisis detection, safety protocols, emergency escalation, or suicide prevention features. Activates for crisis keywords, safety planning, hotline integration, and risk assessment.

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